Temporal and Spatial Patterns in Distemper Virus Cases Reported to SCWDS 1975-2013
Jonathan Wilson
2019-11-29
Summary/Abstract
Canine distemper is an important infectious disease that affects many mammal species. There is evidence of CDV infection in all terrestrial carnivores families and some marine carnivore families. CDV has been detected in wild animal species such as the African lion and Amur tigers and has been responsible for substantial population declines of the animals during outbreaks. First seen in domestic dogs in the late 1970’s, CDV spread through the population rapidly (???). CDV is seen most commonly in domestic cats and dogs but frequent cross species transmission does occur in non-domestic carnivores. In domestic ferrets mortality rates can reach 100%. CDV has been responsible for population declines of endangered mustelids like the black-footed ferret. CDV is also endemic in the eastern U.S. raccoon population. Raccoons are thought to be a reservoir for other wild animals and domestic dogs as well as other species of carnivores. CDV has been found to be persisting in areas like Yellow Stone national park, which has a diverse carnivore population. Multiple outbreaks have occurred in the wolf, coyote and cougar populations Although raccoons are thought to be a major reservoir for CDV, little research has been done to identify the disease dynamics within this population.
Introduction
Canine distemper is an important infectious disease that affects many mammal species. The causative agent, canine distemper virus (CDV) is an enveloped, single stranded, negative sense RNA virus in the Morbillivirus family. Transmitted via the respiratory route, CDV is highly infectious (Deem, Spelman, Yates, & Montali, 2000). There is evidence of CDV infection in all terrestrial carnivores families and some marine carnivore families (Deem et al., 2000). Morbidity and mortality varies depending on the species but closely resembles rabies in wild carnivores (Hoff, Bigler, Proctor, & Stallings, 1974). The Mustelidae family is among the species with the highest fatality rate, while the domestic dog can be a asymptomatic carrier (Deem et al., 2000). CDV has been detected in wild animal species such as the African lion and Amur tigers and has been responsible for substantial population declines of the animals during outbreaks (Roelke-Parker et al., 1996; Seimon et al., 2013).
Canine Distemper Virus In the U.S.
First seen in domestic dogs in the late 1970’s, CDV spread through the population rapidly (Alison et al 2013). CDV is seen most commonly in domestic cats and dogs but frequent cross species transmission does occur in non-domestic carnivores (Allison et al 2013 and (Greene & Appel, 1990). Severity in domestic dogs depends on the animals’ immune status and age in addition to strain virulence (Beineke, Baumgärtner, & Wohlsein, 2015). In the U.S. raccoons (Procyon lotor), foxes (Vulpes vulpes and Urocyon cinereoargenteus), coyotes (Canis latrans), wolves (Canis lupus) , skunks (Mephitis mephitis), badgers (Taxidea taxus), mink (Mustela vison) and ferrets (mustelidae spp.) are among the species susceptible to CDV infection (???; Kapil et al., 2008). In domestic ferrets mortality rates can reach 100%. CDV has been responsible for population declines of endangered mustelids like the black-footed ferret. CDV is also endemic in the eastern U.S. raccoon population. Raccoons are thought to be a reservoir for other wild animals and domestic dogs as well as other species of carnivores (Alison et al 2013, and (Roscoe, 1993). CDV has been found to be persisting in areas like Yellow Stone national park, which has a diverse carnivore population. Multiple outbreaks have occurred in the wolf, coyote and cougar populations (Almberg, Cross, & Smith, 2010; Almberg, Mech, Smith, Sheldon, & Crabtree, 2009). Although raccoons are thought to be a major reservoir for CDV, little research has been done to identify the disease dynamics within this population. Available data is sparse, dated and focuses on individual states and discrete sites. The use of past and current presence only cases allows for spatio-temporal analysis of the CDV in the southeastern United States. The objective of this study was to identify spatial and temporal patters in distemper virus cases reported to the Southeastern Cooperative Wildlife Disease Study from 1975 to 2013.
Description of data and data source
Data was recorded from Canine distemper positive cases submitted to the Southeastern Cooperative Wildlife Disease Study between 1975 and 2013. Cases were identified as CDV by fluorescent antibody testing and/or histologic diagnosis of characteristic lesions. Species, date of submission, county of origin, and sex were noted. A total number of 701 positive cases were submitted from 13 states over the 38-year period. Positive cases were comprised of raccoons (n=462), gray foxes (n=211), striped skunks (n=13), coyotes (n=7), red foxes (n=3), gray wolves (n=3), one mink and a black bear.
Also census and county land area data from census.gov
| Species | n |
|---|---|
| Black Bear | 1 |
| Coyote | 7 |
| Gray Fox | 211 |
| Gray wolf | 3 |
| Mink | 1 |
| Raccoon | 462 |
| Red Fox | 3 |
| Striped Skunk | 13 |
Questions/Hypotheses to be addressed
1.Are there temporal trends in cases diagnosed related to the ecology of the hosts?
2.Are there patterns in the timing of species being diagnosed suggesting cross species infection? (raccoons are considered primary reservoirs, are peaks in raccoon infection followed by other species peaks suggesting spillover)
3.Are there spatial patterns of infection within the southeast relating to landuse?
Methods
Data aquisition
Data of animals brought to SCWDS between 1975 and 2013, which were diagnosed as having CDV at post mortem. Cases were identified as CDV by fluorescent antibody testing and/or histologic diagnosis of characteristic lesions. Species, date of submission, county of origin, and sex were noted. ##Overview of Data Data contained the the follwing varibles….
Data import and cleaning
Detailed description of data analysis and cleaning in supplemtary folder
Time Series analsys
time series analysis and ARIMA model construction was conducted using the “fpp2” package from Forecating: principles and practice, Hyndman & Athanasopoulos.(Hyndman & Athanasopoulos, 2018)
Results
Univariate analysis
Initial probing of the data set revealed the vast majority of cases to be submitted from the state of Georgia. This is understandable as SCWDS is located in Athens, GA. The other feature is that almost all of the submitted cases are Raccoons or Gray Foxes. From this point the data analysis will focus on the state of Georgia and on these two species, Raccoon and Gray Fox. ###Initial Data Probing
Number of cases of CDV per state, submitted to SCWDS, 1075-2013
Map of CDV cases per state submitted to SCWDS, 1975-2013 .
Number of CDV cases per species submitted to SCWDS, 1975-2013
Cases per Year
Bivariate analysis of Species and Age of CDV cases submitted to SCWDS, 1975-2013
Bivariate analysis of Species and Sex of CDV cases submitted to SCWDS, 1975-2013
#```{r, resultfigure3, fig.cap= ‘Species Time’, echo=FALSE, warning=FALSE, message=FALSE}
#```
#```{r, resultfigure3, fig.cap= ‘Species Time’, echo=FALSe, warning=FALSE, message=FALSE}
#```
Use a combination of text/tables/figures to explore and describe your data. You should produce plots or tables or other summary quantities for most of your variables. You definitely need to do it for the important variables, i.e. if you have main exposure or outcome variables, those need to be explored. Depending on the total number of variables in your dataset, explore all or some of the others.
Bivariate analysis
Create plots or tables and compute simple statistics (e.g. t-tests, simple regression model with 1 predictor, etc.) to look for associations between your outcome(s) and each individual predictor variable
Species Time